Help with Frankfurt to Munich itinerary?

I'd have to spend some time looking at your Itinerary, but one point that comes to mind is that it would be a good idea to choose hotels that provide parking. Driving in Munich is not a good idea, so you might have a look at Hotel Uhland, which is located in a quiet residential street. The rooms are comfortable and they serve a great breakfast.

For "must do's" and hotels in other locations, I'd highly recommend picking up a copy of the RS Germany guidebook. The 2017 version should be released in the near future. The books are a wealth of information, and will probably save you money.

I'm not a huge fan of driving after an international flight, but Beedenkirchen isn't very far from the airport. And you'll find yourself in one of my favorite areas of Germany, the Odenwald, which is very difficult to adequately explore via public transportation. Spend a little time driving around some of the small towns in the region (after getting a full night's sleep, of course)... Rothenburg might feel a little redundant afterwards. Where are you sleeping the first night? I've driven through Beedenkirchen several times... there isn't much there, although the scenery is great. If you're looking for a good town to catch a bite to eat and stroll around a bit, check out Heppenheim, about 20 minutes drive away. It has a beautiful market square with several good restaurants, and a castle looking down at you from a nearby mountain.

Within the Odenwald on the way to Rothenburg, at least stop off quickly in Lindenfels (you'll know why when you see it!), and if you have the time, Michelstadt, a very Rothenburg-esque town without the tourist hordes. Oh, and very close to Beedenkirchen is the Felsenmeer (in Lauertal), which is a large boulder formation on the mountain side.

Your direct route of travel more or less goes by Rothenburg, so see it if you must. Just realize that apart from all the trinket shops and tour buses, it isn't nearly as unique as advertised. I personally prefer Dinkelsbühl.

I would ditch the rental car when you arrive in Nürnberg. From there on out, your trip would only be more difficult with a car. Driving and parking (even with a GPS) are an absolute nightmare in Munich. Freising is easy to reach via Sbahn and many hotels offer airport shuttles.

Nürnberg: I have put together an two-hours itinerary for somebody else here:
https://community.ricksteves.com/travel-forum/germany/nuremberg-or-rothenburg

Yes, ditch the car after you get to Nuremberg. It will just get in the way.

Google maps shows a Gasthof-Pension smack in the middle of Beedenkirchen.
In Rothenburg we stayed at the Hotel Gerberhaus, inside the wall (actually just out the back door) and some limited parking in a garage for 10 EUR/nt. Its a RS place, in his guidebook, so modest rooms, decent price, good breakfast.

We liked the Gasthof Goldener Greifen in Rothenburg

http://www.gasthof-greifen-rothenburg.de/english/inn-hotel-rothenburg.html

It is the former home of Rothenburg's most famous mayor, Heinrich Toppler. Good breakfast and plain, good meals. There is parking behind the building. The website says it is free.

In Freising we like Hotel Bayerischerhof.

http://www.bayerischerhof-freising.de/hotel/

It is newly remodeled and just off the main square. You can catch a bus from the train station to the airport. We have also just ordered a taxi. Breakfast is good and served early. We like the Wirthaus Huber for a last, good German meal in country. Reservations are probably better but we always sneak in early without them.

http://www.weissbraeu-huber.de

Last time in Nürnberg we stay at the Art and Business Hotel. It is no smoking. Good breakfast. Nice views of the sculpture garden from the breakfast room.

http://www.art-business-hotel.com/?gclid=CLW5wffm8c0CFQUIaQodwKgFXA.

Thanks for the great suggestions, especially in the Odenwald and hotel recommendations!